Didn't make any difference for me either. I did have partial success with other settings changes though -

(note that my problem appears to be that the sound coming from the front speakers appears to be background/effects sound only - mouths move but no dialog, but you can hear birds tweeting and similar effects)Audio settings (under 'common transcode settings') are set as follows:

As for the audio in the 3 S3 episodes of GOT - this has encoded 5.1ch AC3 sound in the MKV files. If I enable 6ch sound in audio settings and have none of the 'no re-encode' options checked, then it seems to play the rear channels out of the front speakers only - so only effects sounds and no dialog heard. If I enable the first 2 'no re-encode' options, then the sound appears to be fine - this is all when playing under 'MEncoder' (even with the latest revision of MEncoder installed). If I switch to 2 channel sound, then even with the 'no re-encode' options all unchecked, the sound plays fine. So the issue is to do with the way PMS uses MEncoder to re-encode the 5.1ch sound in these files specifically. Several other series with 5.1ch AC3 sound play fine under the default settings, so its just with these GOT episodes where there is an issue - maybe these have been encoded using some new AC3 methods - I really have no idea past the findings above.